Prevalence of Citrus tristeza virus in North Eastern region of India and molecular characterization of its isolates

Incidence of Citrus tristeza virus (CTV) in commercially important citrus species; Khasi mandarin (Citrus reticulata), Assam lemon (Citrus limon) and rough lemon (Citrus jambhiri) in Assam, Meghalaya, Arunachal Pradesh and Nagaland of Northeast (NE) regions of India was studied using double antibody sandwich ELISA (DAS-ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR). Incidence of CTV disease varied with regions and species of citrus. Incidence was more in Assam lemon than in Khasi mandarin and rough lemon. The viral inoculum was found to be more in Assam and rough lemon than in Khasi mandarin as indicated by higher titre of infected samples. Eight CTV isolates from this region were characterized based on sequencing of coat protein (CP) gene. Sequence analysis showed that CP gene of the present CTV isolates shared 95–99% identity among them. Seven CTV isolates AP3, AP5, JRT1, JRT5, N1, N15 and TK1 were found to be phylogenetically related to each other forming one genogroup and isolate TK 5 was different from other isolates forming another group. Although, recombination events are weak, recombination-detecting program RDP3 showed that majorities of the present isolates are putative recombinants.